pestica-to-conn.sh

#! /bin/bash

# This script only works if PESTICA has already been run.

root=/media/INP_MRI_Backup/projects/INP/conectome_inp/analysis/rsfmri


for subject in AD_002 AD_003 AD_006 AD_008 AD_009 AD_010 AD_011 AD_012 AD_013 AD_014 AD_015 AD_016 AD_017 AD_018 AD_019 AD_020 AD_023 AD_024 AD_025 AD_026 AD_027 AD_030 AD_034 AD_035 AD_040 AD_043 AD_045 AD_046 AD_047 AD_048 AD_052 AD_053 AD_056 AD_057 AD_058 AD_060 AD_061 AD_064 AD_066 AD_067 AD_069 AD_070 AD_071 AD_072 AD_073 AD_074 AD_076 AD_080 AD_081 AD_083 AD_091 AD_092 HC_001 HC_004 HC_005 HC_007 HC_021 HC_022 HC_028 HC_029 HC_031 HC_032 HC_033 HC_036 HC_037 HC_038 HC_039 HC_041 HC_042 HC_044 HC_049 HC_050 HC_051 HC_054 HC_055 HC_059 HC_062 HC_063 HC_065 HC_068 HC_075 HC_077 HC_078 HC_082 HC_084 HC_085 HC_086 HC_087 HC_088 HC_093 HC_094 HC_095;

do 

cd $root/preproc/$subject/${subject}_fmri_mc_pestica

echo "CONVERTING SUBJECT $subject"

echo `pwd`

#Volume is the number of slices in a volume. The number of volumes is 300.

matlab $MATLABLINE <<< "card_pestica=dlmread('card_pestica.dat'); volume = 36; card_pestica_vol = arrayfun(@(i) max(card_pestica(i:i+volume-1)),1:volume:length(card_pestica)-volume+1); card_pestica_vol = reshape(card_pestica_vol,[300,1]); save('card_pestica_vol.mat'); dlmwrite('card_pestica_vol.txt',card_pestica_vol);resp_pestica=dlmread('resp_pestica.dat'); volume = 36; resp_pestica_vol = arrayfun(@(i) max(resp_pestica(i:i+volume-1)),1:volume:length(resp_pestica)-volume+1); resp_pestica_vol = reshape(resp_pestica_vol,[300,1]); save('resp_pestica_vol.mat'); dlmwrite('resp_pestica_vol.txt',resp_pestica_vol);exit;"

cp card_pestica_vol.txt $root/physio/${subject}_card.txt
cp resp_pestica_vol.txt $root/physio/${subject}_resp.txt

cd $root

done